My lightning talk at #ievobio 2011

1. Using Treebase from R
Carl Boettiger, @cboettig
UC Davis
June 22, 2011
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 1/18

2. Informatics tools must reflect
current research methods
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 2/18

3. Thank you
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 3/18

4. Graduate Student
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 4/18

5. Methods developer
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 5/18

6. Teacher
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 6/18

7. Bodega Phylogenetics Workshop
http://bodegaphylo.wikispot.org/
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 7/18

8. Bodega Phylogenetics Workshop
No informatics software
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 8/18

9. Bodega Phylogenetics Workshop
almost no internet
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18

10. Bodega Phylogenetics Workshop
almost no internet (we’re fixing that)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18

11. Bodega Phylogenetics Workshop
Students required to bring their own data.
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 10/18

12. Bodega Phylogenetics Workshop
Students required to bring their own data. (we’re proud of that.)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 10/18

13. Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 11/18

14. Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 12/18

15. Why?
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

16. Why?
Education
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

17. Why?
Education Journal club that repeats analyses
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

18. Why?
Education Journal club that repeats analyses
Meta-Analyses
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

19. Why?
Education Journal club that repeats analyses
Meta-Analyses that update themselves
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

20. Why?
Education Journal club that repeats analyses
Meta-Analyses that update themselves
Tools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18

21. See new paper (i.e. Derryberry et al. 2011)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

22. See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into R
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

23. See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into R
Repeat analysis (diversification rate)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

24. See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into R
Repeat analysis (diversification rate)
Compare against newer methods
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

25. See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into R
Repeat analysis (diversification rate)
Compare against newer methods
Compare against similar phylogenies
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

26. See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into R
Repeat analysis (diversification rate)
Compare against newer methods
Compare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->tree
plot(tree); metadata(tree$S.id)
yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18

27. Into the hands of user/developer community
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18

28. Into the hands of user/developer community
Scott Chamberlain
@recology
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18

29. Now in the works
Dryad API
Mendeley, PLoS, Springer APIs
EoL API
...
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 16/18

30. Thanks
Collaborators
Scott Chamberlain (Rice)
Duncan Temple-Lang (UC Davis, R-project)
Advice & Support
Todd Vision, Rutger Vos, Bill Peil, Hilmar Lapp
TreeBASE & Dryad developer lists
Making it possible
Peter Wainwright (interested mentor)
Alan Hastings (advisor)
CSGF (funding)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 17/18

31. https://github.com/cboettig/treeBASE
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 18/18